runSAM: runSAM

In shenorrLab/csSAM: csSAM - cell-specific Significance Analysis of Microarrays

Description

A lightweight version of the SAM algorithm, only performs two group comparison with equal deltas on each tail

Usage

runSAM(G, y, s0.sam = NULL, stand.r = TRUE, stat.only = TRUE)

Arguments

G	Matrix of gene expression, rows ordered in the same order at the cell-frequency matrix (n by p, n samples, p genes)
y	Numeric group association of each sample. Either 1 or 2.
s0.sam	Input or computed value of SAM exchangeability factor. Default is determined automatically
stand.r	Median center and standardize arrays. Default is TRUE.
stat.only	logical that indicates if only the SAM statistic should be returned, or a list containing a statistic matrix (SAM statistic, effect size and standard deviation) and the SAM exchangeability factor used in the computation.

Author(s)

Shai Shen-Orr, Rob Tibshirani, Narasimhan Balasubramanian, David Wang

References

Shen-Orr SS, Tibshirani R, Khatri P, Bodian DL, Staedtler F, Perry NM, Hastie T, Sarwal MM, Davis MM and Butte AJ (2010). “Cell type-specific gene expression differences in complex tissues.” Nature methods, 7(4), pp. 287-9. ISSN 1548-7105, doi: 10.1038/nmeth.1439 (URL: http://doi.org/10.1038/nmeth.1439).

shenorrLab/csSAM documentation built on May 29, 2019, 9:23 p.m.